Ageing impact in gene expression on skeletal muscle repair
Bioinformatic analysis : differential expression genes part
Team Le Grand
02 mai,2022
I.Data origine (Mus musculus - tibialis anterior muscle)
In order to explore cell expression during muscle regeneration in young(2-3 months) and old(18-22 months) cells, RNAseq experiments were performed using cells sorted and FACs at four time points:
- D0 muscles without injury
- D2, 2 days after cardiotoxin-induced injury
- D4, 4 days after injury
- D7, 7 days after injury
The cell types sampled were as follows:
- D0 , Endothelial Cells ECs, FibroAdipogenic Progenitors - FAPs, Muscle Stem Cells MuSCs.
- D2 , ECs, FAPs, MuSCs., Neutrophile Cells, Inflammatory Macrophages - Inflammatory-Mac and Resolving Macrophages - Resolving-Mac .
- D4, ECs, FAPs, MuSCs, Inflammatory-Mac, Resolving-Mac
- D7, ECs, FAPs, MuSCs, Resolving-Mac
I.1 Pretreatment RNA-seq data with pipeline nfcore/rnaseq (v.1.4.2)
The RNA-seq data is aligned to the GRCm38 genome with STAR and counted with FeatureCount .
Only transcripts associated with coding proteins are kept.
Differentially expressed genes (DEG) processed with DESeq2_1.30.1 old vs young (reference expression is young one), for each cell type at each time Day_TypeCell_Old vs Day_TypeCell_Young
II.Overview of DEG significant analysis
On any given day and cell type there are 4499 genes differentilly expressed with a good confidence (padj<=0.05) (= DEG significative) on 17797 genes expressed in total or 25% of DEG significant.
The table below, is the percent of DEG significant on total genes expressed.
| D0 | D2 | D4 | D7 | PercentDEGSigniOnTyCell | |
|---|---|---|---|---|---|
| ECs | 2 | 1.3 | 6.2 | 13.7 | 19.1 |
| FAPs | 11.5 | 5.3 | 8.7 | 9.1 | 25.9 |
| MuSCs | 10.6 | 42.3 | 30.7 | 13.3 | 72.8 |
| Inflammatory-Mac | NA | 0.7 | 0.4 | NA | 1 |
| Neutrophils | NA | 6.9 | NA | NA | 6.9 |
| Resolving-Mac | NA | 2.1 | 0.8 | 3.1 | 5.3 |
| PercentDEGSigniOnDay | 21.7 | 54.1 | 42.2 | 32.8 | NA |
Graphics and tables are in /home/bioinfo/BulkAnalysis_plusNetwork/exam_INTER_conditions/static/
III.Exploration of DEG significant patterns in one type cell on muscle repair
This exploration is type cell specific and focus on gene differentially expressed significant (padj<0.05) On one type Cell, we observe different dynamics of differential expression across days
- For some gene, the difference between Old and Young are specific of one day, on one step of muscle regeneration.
- For some gene, the difference is always present, no specific.
- For some gene, the age up his expression in some days and down in other day.
| one.Day | two.Day | three.Day | four.Day | |
|---|---|---|---|---|
| Number Gene DE on | 4489 | 1170 | 208 | 35 |
| Pourcent Gene DE on | 76 | 20 | 4 | 0 |
III.1 Sankey plot - Show the days pattern of DEG
Group by number of day DEG significant
Group by combination of days DEG significant
III.2 Sankey plot - Show the days pattern of DEG UP and DOWN significant
ECs
Group by combination of number of days DEG UP and DOWN significant
Group by number of day DEG UP and DOWN significant
Group by combination of days DEG UP and DOWN significant
Table with pattern the most present
FAPs
Group by combination of number of days DEG UP and DOWN significant
Group by number of day DEG UP and DOWN significant
Group by combination of days DEG UP and DOWN significant
Table with pattern the most present
MuSCs
Group by combination of number of days DEG UP and DOWN significant
Group by number of day DEG UP and DOWN significant
Group by combination of days DEG UP and DOWN significant
Table with pattern the most present
Inflammatory-Mac
Group by combination of number of days DEG UP and DOWN significant
Group by number of day DEG UP and DOWN significant
Group by combination of days DEG UP and DOWN significant
Table with pattern the most present
Resolving-Mac
Group by combination of number of days DEG UP and DOWN significant
Group by number of day DEG UP and DOWN significant
Group by combination of days DEG UP and DOWN significant
